nmr-processing 9.3.6 → 9.3.8-pre.1681135907

package/src/xyz/util/fft2d/digitalFilter.ts

@@ -0,0 +1,24 @@
+import { DataReIm } from 'ml-spectra-processing';
+
+export function digitalFilter(
+  data: DataReIm,
+  options: { digitalFilterValue: number },
+) {
+  let { digitalFilterValue = 0 } = options;
+  let re = new Float64Array(data.re);
+  let im = new Float64Array(data.im);
+
+  let pointsToShift = Math.floor(digitalFilterValue);
+
+  const skip = 0;
+  pointsToShift += 0;
+
+  const newRe = new Float64Array(re.length);
+  const newIm = new Float64Array(im.length);
+  newRe.set(re.slice(pointsToShift));
+  newRe.set(re.slice(skip, pointsToShift), re.length - pointsToShift);
+  newIm.set(im.slice(pointsToShift));
+  newIm.set(im.slice(skip, pointsToShift), im.length - pointsToShift);
+
+  return { re: newRe, im: newIm };
+}

package/src/xyz/util/fft2d/fftDirectDimension.ts

@@ -0,0 +1,111 @@
+import { DoubleArray } from 'cheminfo-types';
+import Matrix from 'ml-matrix';
+import {
+  reimAutoPhaseCorrection,
+  reimFFT,
+  reimPhaseCorrection,
+} from 'ml-spectra-processing';
+
+import {
+  apodization,
+  ApodizationOptions,
+} from '../../../apodization/apodization';
+
+import { digitalFilter } from './digitalFilter';
+import { removeDCOffset } from './removeDCOffset';
+import { zeroFilling, ZeroFillingOptions } from './zeroFilling';
+
+interface PhaseCorrection {
+  mode?: string;
+  ph0?: number;
+  ph1?: number;
+}
+
+export interface DirectDimensionOptions {
+  fnMode?: string;
+  digitalFilterValue?: number;
+  zeroFilling?: ZeroFillingOptions;
+  apodization?: ApodizationOptions;
+  phaseCorrection?: PhaseCorrection;
+}
+
+export function fftDirectDimension(
+  data: { re: DoubleArray[]; im: DoubleArray[] },
+  options: DirectDimensionOptions,
+) {
+  const { re: reData, im: imData } = data;
+  const nbRows = reData.length;
+  const nbColumns = reData[0].length;
+
+  const { zeroFilling: zeroFillingF2, digitalFilterValue = 0 } = options;
+
+  const { factor: f2Factor = 2 } = zeroFillingF2 || {};
+  const nbPointsF2 =
+    zeroFillingF2?.nbPoints || 2 ** Math.round(Math.log2(nbColumns * f2Factor));
+
+  const reFFT = new Matrix(nbRows, nbPointsF2);
+  const imFFT = new Matrix(nbRows, nbPointsF2);
+
+  const { apodization: apodizationF2 } = options;
+  let {
+    ph0: ph0F2,
+    ph1: ph1F2,
+    mode: pcModeF2 = 'no',
+  } = options?.phaseCorrection || {};
+
+  for (let i = 0; i < nbRows; i++) {
+    const newData = digitalFilter(
+      { re: reData[i], im: imData[i] },
+      { digitalFilterValue },
+    );
+
+    Object.assign(newData, removeDCOffset(newData, { digitalFilterValue }));
+
+    if (apodizationF2) {
+      const { re: aRe, im: aIm } = apodization(newData, apodizationF2);
+      Object.assign(newData, { re: aRe, im: aIm });
+    }
+
+    Object.assign(
+      newData,
+      zeroFilling(newData, { digitalFilterValue, nbPoints: nbPointsF2 }),
+    );
+
+    Object.assign(newData, reimFFT(newData, { applyZeroShift: true }));
+
+    const dfResidual =
+      (digitalFilterValue - Math.round(digitalFilterValue)) * Math.PI * 2;
+    if (dfResidual > 0) {
+      Object.assign(newData, reimPhaseCorrection(newData, 0, -dfResidual));
+    }
+
+    if (
+      i === 0 &&
+      pcModeF2 === 'pk' &&
+      ph0F2 === undefined &&
+      ph1F2 === undefined
+    ) {
+      const phased = reimAutoPhaseCorrection(newData, { magnitudeMode: false });
+      ph0F2 = phased.ph0;
+      ph1F2 = phased.ph1;
+    }
+    if (pcModeF2 === 'pk' && ph0F2 !== undefined && ph1F2 !== undefined) {
+      Object.assign(
+        newData,
+        reimPhaseCorrection(
+          newData,
+          (ph0F2 * Math.PI) / 180,
+          (ph1F2 * Math.PI) / 180,
+        ),
+      );
+    }
+
+    reFFT.setRow(i, newData.re);
+    imFFT.setRow(i, newData.im);
+  }
+
+  return {
+    re: reFFT,
+    im: imFFT,
+  };
+}

package/src/xyz/util/fft2d/fftIndirectDimension.ts

@@ -0,0 +1,123 @@
+import { DoubleArray } from 'cheminfo-types';
+import Matrix from 'ml-matrix';
+import {
+  reimAbsolute,
+  reimAutoPhaseCorrection,
+  reimFFT,
+  reimPhaseCorrection,
+} from 'ml-spectra-processing';
+
+import {
+  apodization,
+  ApodizationOptions,
+} from '../../../apodization/apodization';
+
+import { zeroFilling, ZeroFillingOptions } from './zeroFilling';
+
+interface PhaseCorrection {
+  mode?: string;
+  ph0?: number;
+  ph1?: number;
+}
+
+export interface IndirectDimensionOptions {
+  fnMode?: string;
+  zeroFilling?: ZeroFillingOptions;
+  apodization?: ApodizationOptions;
+  phaseCorrection?: PhaseCorrection;
+}
+
+export function fftIndirectDimension(
+  data: { re: DoubleArray[] | Matrix; im: DoubleArray[] | Matrix },
+  options: IndirectDimensionOptions,
+) {
+  const reData = Matrix.checkMatrix(data.re);
+  const imData = Matrix.checkMatrix(data.im);
+
+  const nbRows = reData.rows;
+  const nbColumns = reData.columns;
+
+  const { zeroFilling: zeroFillingF1 } = options;
+  const { factor: f1Factor = 2 } = zeroFillingF1 || {};
+  const nbPointsF1 =
+    zeroFillingF1?.nbPoints || 2 ** Math.round(Math.log2(nbRows * f1Factor));
+  const { apodization: apodizationF1 } = options;
+  let {
+    ph0: ph0F1,
+    ph1: ph1F1,
+    mode: pcModeF1,
+  } = options.phaseCorrection || {};
+
+  const reResult = new Matrix(nbPointsF1, nbColumns);
+  const imResult = new Matrix(nbPointsF1, nbColumns);
+  for (let i = 0; i < nbColumns; i++) {
+    const { re: aRe, im: aIm } = apodization(
+      {
+        re: reData.getColumn(i),
+        im: imData.getColumn(i),
+      },
+      apodizationF1,
+    );
+
+    const newRe = [];
+    const newIm = [];
+    if (options.fnMode === 'echo') {
+      for (let j = 0; j < aRe.length; j += 2) {
+        newRe.push(aRe[j]);
+        newIm.push(aRe[j + 1]);
+      }
+    } else {
+      for (let j = 0; j < aRe.length; j++) {
+        newRe.push(aRe[j]);
+        newIm.push(-aIm[j]);
+      }
+    }
+
+    let transformed = reimFFT(
+      zeroFilling(
+        {
+          re: newRe,
+          im: newIm,
+        },
+        { digitalFilterValue: 0, nbPoints: nbPointsF1 },
+      ),
+      { applyZeroShift: true },
+    );
+    let { re, im } = transformed;
+
+    if (options.phaseCorrection?.mode === 'mc') {
+      re = reimAbsolute({ re, im });
+      im = new Float64Array(im.length);
+    }
+
+    if (pcModeF1 === 'pk') {
+      if (i === 0 && ph0F1 === undefined && ph1F1 === undefined) {
+        //here we can improve it by checking if the experiment is phase sensitive.
+        const phased = reimAutoPhaseCorrection(
+          { re, im },
+          { magnitudeMode: false },
+        );
+        ph0F1 = phased.ph0;
+        ph1F1 = phased.ph1;
+      }
+      if (ph0F1 !== undefined && ph1F1 !== undefined) {
+        Object.assign(
+          transformed,
+          reimPhaseCorrection(
+            transformed,
+            (ph0F1 * Math.PI) / 180,
+            (ph1F1 * Math.PI) / 180,
+          ),
+        );
+      }
+    }
+
+    reResult.setColumn(i, re);
+    imResult.setColumn(i, im);
+  }
+
+  return {
+    re: reResult,
+    im: imResult,
+  };
+}

package/src/xyz/util/fft2d/removeDCOffset.ts

@@ -0,0 +1,19 @@
+import { DataReIm, xMean } from 'ml-spectra-processing';
+
+export function removeDCOffset(data: DataReIm, options: any) {
+  let { digitalFilterValue = 0 } = options;
+  const nbPoints = data.re.length;
+  const newRe = new Float64Array(data.re);
+  const newIm = new Float64Array(data.im);
+  const averageRe = xMean(
+    data.re.slice((nbPoints * 0.75) >> 0, nbPoints - digitalFilterValue),
+  );
+  const averageIm = xMean(
+    data.im.slice((nbPoints * 0.75) >> 0, nbPoints - digitalFilterValue),
+  );
+  for (let i = digitalFilterValue; i < nbPoints - digitalFilterValue; i++) {
+    newRe[i] -= averageRe;
+    newIm[i] -= averageIm;
+  }
+  return { re: newRe, im: newIm };
+}

package/src/xyz/util/fft2d/zeroFilling.ts

@@ -0,0 +1,39 @@
+import { DataReIm } from 'ml-spectra-processing';
+
+export interface ZeroFillingOptions {
+  nbPoints?: number;
+  factor?: number;
+  digitalFilterValue?: number;
+}
+
+export function zeroFilling(data: DataReIm, options: ZeroFillingOptions) {
+  let { nbPoints, factor = 2, digitalFilterValue: grpdly = 0 } = options;
+
+  if (!nbPoints) {
+    nbPoints = 2 ** Math.round(Math.log2(data.re.length * factor));
+  }
+
+  let pointsToShift;
+  if (grpdly > 0) {
+    pointsToShift = Math.floor(grpdly);
+  } else {
+    pointsToShift = 0;
+  }
+
+  const { re, im } = data;
+
+  let newRE = new Float64Array(nbPoints);
+  let newIM = new Float64Array(nbPoints);
+
+  const length = Math.min(nbPoints, re.length);
+
+  newRE.set(re.slice(0, length - pointsToShift));
+  newIM.set(im.slice(0, length - pointsToShift));
+
+  if (pointsToShift > 0 && pointsToShift < nbPoints) {
+    newRE.set(re.slice(re.length - pointsToShift), nbPoints - pointsToShift);
+    newIM.set(im.slice(re.length - pointsToShift), nbPoints - pointsToShift);
+  }
+
+  return { re: newRE, im: newIM };
+}

package/src/xyz/xyzBidimensionalFFT.ts

@@ -0,0 +1,123 @@
+import { DoubleArray } from 'cheminfo-types';
+import Matrix from 'ml-matrix';
+
+import { ApodizationOptions } from '../apodization/apodization';
+import { Data2D, Data2DFid } from './Data2D';
+
+import { quadrature } from './quadrature';
+import {
+  DirectDimensionOptions,
+  fftDirectDimension,
+} from './util/fft2d/fftDirectDimension';
+import {
+  fftIndirectDimension,
+  IndirectDimensionOptions,
+} from './util/fft2d/fftIndirectDimension';
+import { ZeroFillingOptions } from './util/fft2d/zeroFilling';
+
+type Info2D = any;
+
+interface BidimensionalFFTOptions {
+  fnMode: string;
+  info: Info2D;
+  zeroFilling?: ZeroFillingOptions;
+  phaseCorrection?: { ph0: number; ph1: number };
+  digitalFilterValue?: number;
+  apodization?: ApodizationOptions;
+  indirect?: IndirectDimensionOptions;
+  direct?: DirectDimensionOptions;
+}
+
+export function xyzBidimensionalFFT(
+  data: Data2D,
+  options: BidimensionalFFTOptions,
+) {
+  ensureData2DFid(data);
+
+  const {
+    info,
+    fnMode,
+    digitalFilterValue = 0,
+    zeroFilling: zeroFillingGeneral,
+  } = options;
+
+  const orderedData = quadrature(data, { fnMode });
+
+  const { re: reData } = orderedData;
+  const nbRows = reData.length;
+  const nbColumns = reData[0].length;
+  const { direct = {}, indirect = {} } = options;
+
+  const { zeroFilling: zeroFillingF2 = zeroFillingGeneral } = direct;
+
+  const { factor: f2Factor = 2 } = zeroFillingF2 || {};
+  const nbPointsF2 =
+    zeroFillingF2?.nbPoints || 2 ** Math.round(Math.log2(nbColumns * f2Factor));
+
+  const transformed = fftDirectDimension(orderedData, {
+    ...direct,
+    fnMode,
+    digitalFilterValue,
+    zeroFilling: { nbPoints: nbPointsF2 },
+  });
+
+  const { zeroFilling: zeroFillingF1 } = options;
+  const { factor: f1Factor = 2 } = zeroFillingF1 || {};
+  const nbPointsF1 =
+    zeroFillingF1?.nbPoints || 2 ** Math.round(Math.log2(nbRows * f1Factor));
+  const { re: reResult, im: imResult } = fftIndirectDimension(transformed, {
+    ...indirect,
+    fnMode,
+    zeroFilling: { nbPoints: nbPointsF1 },
+  });
+
+  const minMaxXY = getMinMaxXY(info);
+  return {
+    re: {
+      z: convertToDoubleArray(reResult),
+      maxZ: reResult.max(),
+      minZ: reResult.min(),
+      ...minMaxXY,
+    },
+    im: {
+      z: convertToDoubleArray(imResult),
+      maxZ: imResult.max(),
+      minZ: imResult.min(),
+      ...minMaxXY,
+    },
+  };
+}
+
+function ensureData2DFid(data: Data2D): asserts data is Data2DFid {
+  if (!('re' in data)) {
+    throw new Error('bidimensional FFT only can be applied to raw data');
+  }
+}
+
+function convertToDoubleArray(data: Matrix) {
+  const result: DoubleArray[] = new Array(data.rows);
+  for (let i = 0; i < data.rows; i++) {
+    result[i] = new Float64Array(data.getRow(i));
+  }
+  return result;
+}
+
+function getMinMaxXY(info: Info2D) {
+  const min: number[] = [];
+  const max: number[] = [];
+  for (let i = 0; i < info.baseFrequency.length; i++) {
+    const baseFrequency = Number.parseFloat(info.baseFrequency[i]);
+    const frequencyOffset = Number.parseFloat(info.frequencyOffset[i]);
+    const spectralWidth = Number.parseFloat(info.spectralWidth[i]);
+    const offset = frequencyOffset / baseFrequency;
+    min.push(offset - spectralWidth * 0.5);
+    max.push(offset + spectralWidth * 0.5);
+  }
+
+  return {
+    minX: min[0],
+    maxX: max[0],
+    minY: min[1],
+    maxY: max[1],
+  };
+}